ngsqc

This is the documentation of ngsqc.

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Contents

License

Copyright 2017 KongDeju

Developers

Changelog

Version 0.1

  • Feature A added
  • FIX: nasty bug #1729 fixed
  • add your changes here!

ngsqc

ngsqc package

Subpackages
ngsqc.arranger package
Submodules
ngsqc.arranger.arranger module
class ngsqc.arranger.arranger.arranger(prefix)[source]
Parameters:prefix (dict) – some description of this dict { “key1”: “….” “key2”: “…” }
Returns:some description of this dict
Return type:dict
arrFastp()[source]
arrFastqc()[source]
arrange()[source]
Module contents
ngsqc.bamqc package
Submodules
ngsqc.bamqc.BamQC module
class ngsqc.bamqc.BamQC.BamQC(bam, prefix)[source]
Module contents
ngsqc.fastqc package
Submodules
ngsqc.fastqc.FastQC module

This is the beginning of Fastq

class ngsqc.fastqc.FastQC.FastQC(fqs, prefix)[source]

init the FastQC class

Parameters:
  • fq (str) – this is the input fastq file
  • prefix (str) – the output prefix
byfastp()[source]

the docstring is cool

byfastqc()[source]
ngsqc.fastqc.fast_qc module
ngsqc.fastqc.fast_qc.qc(fqs, prefix)[source]
ngsqc.fastqc.fastp module
ngsqc.fastqc.fastp.qc(fqs, prefix)[source]

information for qc

ngsqc.fastqc.fastp2table module
ngsqc.fastqc.fastp2table.fastp2table(jsons, prex)[source]
Module contents
ngsqc.reporter package
Submodules
ngsqc.reporter.render module
class ngsqc.reporter.render.Argsor(report)[source]
convert_table(table)[source]
get_images()[source]
get_table()[source]
ngsqc.reporter.render.main(report, template, out)[source]
ngsqc.reporter.render.render(template, args)[source]
ngsqc.reporter.reporter module
ngsqc.reporter.reporter.report(reportDir, prefix)[source]
Module contents
ngsqc.vcfqc package
Submodules
ngsqc.vcfqc.VcfQC module
class ngsqc.vcfqc.VcfQC.VcfQC(vcf, prefix)[source]
Module contents
Submodules
ngsqc.config.py module
Module contents

Indices and tables